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<a href="http://www.rhul.ac.uk/computerscience">Department of Computer Science</a> 
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<h1>
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ClusterONEWeb
<div class="subtitle">A web server implementing <strong>ClusterONE</strong> (<em>Clustering with Overlapping Neighbourhood Expansion</em>)</div>
</h1>

<div class="references">References</div>

If you use this server, please consider citing at least one of these two publications:

<ul>
<li>T. Nepusz, H. Yu, and A. Paccanaro. <a href="http://www.nature.com/nmeth/journal/v9/n5/full/nmeth.1938.html">Detecting overlapping protein complexes in protein-protein interaction networks</a>, <em>Nature Methods</em>, <strong>9</strong>, pp. 471-472, 2012. (<a href="http://www.ncbi.nlm.nih.gov/pubmed/22426491">PubMed</a>)</li>
<li>T. Nepusz, A. E. Romero, and A. Paccanaro. ClusterONEWeb, a web server for predicting protein complexes in PPI networks, <em>in preparation.</em></li>
</ul>

The source code of this server is free software released under the <a href="http://www.gnu.org/copyleft/gpl.html">GPL v3.0</a> and can be downloaded from <a href="https://github.com/ntamas/cl1">GitHub</a>.


<ul id="errors" class="message-container">
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<ol id="steps">
  <li>
    <div class="title">Upload your data file</div>
    <div class="contents">
      <p>Select your data file on your local hard drive by clicking on the button below.</p>
      <p>The data file must be in a simple symbolic weighted edge list format, which looks
      like this:</p>
      <pre>protein1 protein2 weight
protein1 protein3 weight
protein1 protein4 weight
protein2 protein4 weight
...</pre>
      <p>Protein IDs must not contain spaces. The columns must be separated by whitespace characters.
      Weights may be omitted; edges not having an associated weight will be considered as having
      unit weight.</p>   
      <div class="buttons">
        <button id="upload-button"><img src="img/upload.png" width="16" height="16" alt="" />Click here to start uploading</button>
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  </li>
  <li>
    <div class="title">Set the algorithm parameters</div>
    <div class="contents">
    <form id="algorithm_parameters" action="">
      <p>Place the mouse over the question marks to get help on each parameter. The default parameters are recomended for a quick start.</p>

      <fieldset>
        <legend>Basic parameters</legend>
        <div>
          <label for="min_size">Minimum cluster size:</label>
          <input class="positive_integer required" id="min_size" name="min_size" value="3" />
<span class="toolTip" title="Clusters with less than this number of proteins will be not shown (default: 3)">&nbsp;</span>
        </div>
        <div>
          <label for="min_density">Minimum cluster density:</label>
          <input class="number_01 required" id="min_density" name="min_density" value="0.35" />
<span class="toolTip" title="Clusters with a density lower than this threshold (default: 0.35) will be not shown">&nbsp;</span>
        </div>
      </fieldset>
      <fieldset>
        <legend>Advanced parameters</legend>
        <div>
          <label for="node_penalty">Node penalty:</label>
          <input class="nonnegative_float required" id="node_penalty" name="node_penalty" value="2" />
          <span class="toolTip" title="This is the parameter 'p' in the original algorithm. A higher number penalizes the clusters with more proteins (default: 2)">&nbsp;</span>  
        </div>
        <div>
          <label for="merging_method">Merging method:</label>
          <select name="merging_method" id="merging_method">
            <option value="match">Match coefficient</option>
            <option value="meet/min">Meet/min coefficient</option>
          </select>
          <span class="toolTip" title="Under which criterion two clusters should be merged (default: 'Match coefficient')">&nbsp;</span>
        </div>
        <div>
          <label for="similarity">Similarity function:</label>
          <select name="similarity" id="similarity">
            <option value="match">Match coefficient</option>
            <option value="jaccard">Jaccard similarity</option>
            <option value="dice">Dice similarity</option>
            <option value="simpson">Simpson coefficient</option>
          </select>
          <span class="toolTip" title="Similarity function to compare two clusters and result, eventually, in the merge of them (default: 'Match coefficient')">&nbsp;</span>
        </div>
        <div>
          <label for="overlap_threshold">Overlap threshold:</label>
          <input class="number_01 required" id="overlap_threshold" name="overlap_threshold" value="0.8" />
          <span class="toolTip" title="Maximum similarity allowed between to clusters to be joined together (default: 0.8)">&nbsp;</span>
        </div>
        <div>
          <label for="seeding_method">Seeding method:</label>
          <select name="seeding_method" id="seeding_method">
            <option value="unused_nodes">From unused nodes</option>
            <option value="every_node">From every node</option>
            <option value="every_edge">From every edge</option>
          </select>
          <span class="toolTip" title="Method to start a new cluster (default: 'From unused nodes')">&nbsp;</span>
        </div>
      </fieldset>
    </form>
      <div class="buttons">
        <button id="start-button"><img src="img/start.png" width="16" height="16" alt="" />Start the analysis</button>
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  </li>
  <li>
    <div class="title">Examine the results</div>
    <a name="topOfTable"></a>
    <div class="contents">
      <p>Click on the table headers to sort the results.</p>      
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        <button id="download-button"><img src="img/download.png" width="16" height="16" alt="" />Download results</button>
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      <p>Click <a href="#topOfTable">here</a> to go back to the top of the table</p>
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